[BioC] From eSet to AffyBatch Object

[Martin Morgan]

Hi Boris --

Boris Umylny <umylny at apbri.org> writes:

> Hi,
>
> I am working with affy library from Bioconductor 2.3.
>
> The library contains functions (hist, image and boxplot) that work directly on 
> AffyBatch object, but apparently not on ExpressionSet/eSet object.  After I 
> use rma, expresso or mas5 to do background correction and normalization I get 
> an eSet object, which appears to be incompatible with these functions.  If I 
> call hist(exprs(e)), where e is an ExpressionSet object, I get a plot of the 
> first array only. 
>
> Is there a Bioconductor library (other than geneplotter which apparently does 
> not) that provides these functions on eSet/ExpressionSet object?

Others will probably point to specific packages implementing plotting
methods for expression data, but I find myself doing things more
directly, typically using the lattice package

  library(lattice)
  library(Biobase)
  data(sample.ExpressionSet)
  eset <- sample.ExpressionSet   # easier to type!
  df <- data.frame(Expression=as.vector(exprs(eset)),
                   Sample=sampleNames(eset)[col(eset)])
  densityplot(~log2(Expression)|Sample, df, plot.points=FALSE)

or

  densityplot(~log2(Expression), group=Sample, df, plot.points=FALSE)

> Is there a way to get an AffyBatch object from eSet object to make use of 
> these functions?

An AffyBatch and an ExpressionSet are conceptually different ('raw'
vs. preprocessed data) so trying to convert back and forth at will
doesn't really make sense.

Martin

> Thank you in advance for your help.
>
>
> Sincerely,
>
>
> Boris Umylny
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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